Yes. Any updates during the alpha/beta with significant content changes will not maintain save compatibility (after release, all updates will).
You can delay updating until you are done your current playthrough, though, if there is one mid-game, or revert to a previous version in Galaxy (or by manually reinstalling, if you kept the downloaded installer, and not applying the latest patch).
In terms of an eventual restart, you wouldn't be able to play from an alpha save after the game is released.